Intro to Galaxy Administration @ Barcelona

2-6 March 2020

• Timetable
  • Monday
  • Tuesday
  • Wednesday
  • Thursday
  • Friday
• Admin Training Materials
• Join the Discussion
• Galaxy Training Materials

Location, Logistics, and Registration

This training will be offered 2-6 March at the Barcelona Supercomputing Center.

See the workshop's Galaxy Community Hub page for details on logistics and registration.

Training VM instances

Galaxy training instances will be bootstrapped with a small Ansible playbook, which you may find useful for repeating the exercises at home using a VM, Docker image, etc.

Important Links

• Q&A!
• https://gxy.io/gatchat - Chat for this workshop
• https://gxy.io/gatmachines - VMs

Timetable

Timetable with sessions and material is being continuously updated. This is NOT final.

Monday

This day covers getting a Galaxy server setup with Ansible, a server you will develop for the rest of the week.

2nd March

Time	Topic	Slides	Exercises	Instructor
08:30	Registration
09:00	Welcome and introduction	Welcome		All
09:20	Deployment and platform options	Deployment		M
09:40	Intro to Ansible	Ansible	Exercise	Ni
10:30	Break (coffee & snacks)
10:45	Galaxy Server Part 1: Basic Install	Galaxy Install, Database, uWSGI	Exercise	H, M, Na
13:00	Lunch (catered)
14:00	Galaxy Server Part 2: Towards Production	systemd		H, Na
15:30	Break (coffee & snacks)
15:50	Galaxy Server Part 3: Advanced Install	Production		H, Na
16:45	Close Day 1
17:00	Guided tour of the Supercomputing facility

Tuesday

3rd March

Today we pivot to focus on making that server useful: adding tools and data, configuring quotas and authentication

Time	Topic	Slides	Exercises	Instructor
09:00	Welcome and questions
09:15	Galaxy Tool Shed	Toolshed		M
10:00	Ephemeris	Ephemeris	Exercise	Ni
10:30	Break (coffee & snacks)
10:50	Ephemeris: Continued
12:00	Users, Groups, and Quotas	Slides		S
13:00	Lunch (catered)
14:00	Reference Data	Slides	CVMFS Exercise	Na
16:15	External authentication	Slides	Upstream Auth Exercise	H
17:00	Close Day 2

Wednesday

4th March

Now that your server has some bells and whistles, let's connect it to a compute cluster, and learn about the job configuration file.

Time	Topic	Slides	Exercises	Instructor
09:00	Welcome and questions
09:15	Exploring the Galaxy job configuration file	Slides	job_conf.xml	M
09:45	Connecting Galaxy to a compute cluster	Slides	Exercise	Na
10:20	Break (coffee & snacks)
10:40	Compute cluster (continued)
12:00	Compute Resources: Continued			Na
13:00	Lunch
15:15	Break (coffee & snacks)
15:35	Pulsar	Slides	Exercise	H
17:00	Close day 3

Thursday

5th March

Today is a bit of a grab-bag, we'll cover stuff interactive tools, bioblend (galaxy API library), and then go back to admin focused issues of monitoring.

Time	Topic	Slides	Exercises	Instructor
09:00	Welcome and questions
09:15	Interactive Tools		Exercise	Na
10:45	Break (coffee & snacks)
11:00	Bioblend			Ni
12:00	Storage management	Slides	Exercise	Ni
13:00	Lunch (catered)
14:00	Monitoring Part 1: Reports		Reports Exercise	M
14:35	Monitoring Part 2: Telegraf, InfluxDB, Grafana	Slides	Telegraf Exercise	S
15:15	Break (coffee & snacks)
15:30	Monitoring Part 3: DB queries, command line & scripts	Slides	gxadmin	H
17:00	Wrap up and close

Friday

6th March

The last day! We made it. Even more assorted topics

Time	Topic	Slides	Exercises	Instructor
09:00	Welcome and questions
09:15	What's new in Galaxy? (2019 edition)	Slides		M
10:15	Break (coffee & snacks)
10:30	TIaaS		TIaaS Exercise	H & S
11:30	Upgrading Galaxy	Slides		Ni
12:00	When things go wrong: Galaxy Server Troubleshooting	Slides		Na
13:00	Lunch (catered)
Spare Time	Extra Topics
15:00	Wrap up and close

Instructors

• (H)elena Rasche - Galaxy Europe
• (S)askia Hiltemann - Erasmus Medical Center, the Netherlands
• (Na)te Coraor - Galaxy Project, Penn State University, United States
• (M)arius van den Beek - Galaxy Project, Penn State University, Europe
• (Ni)cola Soranzo - Earlham Institute